+Open data
-Basic information
Entry | Database: PDB / ID: 1kni | ||||||
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Title | Stabilizing Disulfide Bridge Mutant of T4 Lysozyme | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / Glycosidase / Bacteriolytic enzyme | ||||||
Function / homology | Function and homology information viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / Rigid body / Resolution: 1.7 Å | ||||||
Authors | Jacobson, R.H. / Matsumura, M. / Faber, H.R. / Matthews, B.W. | ||||||
Citation | Journal: Protein Sci. / Year: 1992 Title: Structure of a stabilizing disulfide bridge mutant that closes the active-site cleft of T4 lysozyme. Authors: Jacobson, R.H. / Matsumura, M. / Faber, H.R. / Matthews, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kni.cif.gz | 47.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kni.ent.gz | 33 KB | Display | PDB format |
PDBx/mmJSON format | 1kni.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/1kni ftp://data.pdbj.org/pub/pdb/validation_reports/kn/1kni | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18632.441 Da / Num. of mol.: 1 / Mutation: T21C,T142C,C54T,C97A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-BME / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.93 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Ambient pressure: 101 kPa / Mean temperature: 298 K |
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Diffraction source | Source: rotating-anode X-ray tube / Type: ELLIOTT GX-21 / Wavelength: 1.5418 Å / Target: Cu / Voltage: 40 kV |
Detector | Type: OSCILLATION CAMERA / Detector: photographic film / Date: Jul 1, 1991 / Details: Kodak No-Screen X-ray film |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 1.5418 Å |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.7 Å / Num. obs: 15778 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.071 |
-Processing
Software |
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Refinement | Method to determine structure: Rigid body Starting model: WT* T4 lysozyme Highest resolution: 1.7 Å / Isotropic thermal model: Isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: residues 163 and 164 are missing in the electron density.
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Refinement step | Cycle: LAST / Highest resolution: 1.7 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / σ(F): 0 / Rfactor all: 0.176 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_deg / Dev ideal: 2.9 |